[Neurodebian-devel] Debian packages for Stimfit

[Yaroslav Halchenko]

Hi Christoph,

> > > * since stimfit ships python module, to be friendly to Debian python
> >  guys, might be useful to add
> No, there's no standalone stimfit Python module. _stf.so can only be
> imported from the embedded Python shell in a running stimfit application.

if someone becomes pedantic (e.g. like Debian ftpmasters do from time to time
;)), you might be asked then to ship stimfit module elsewhere, e.g. directly
under /usr/lib/stimfit since /usr/lib/python2.6/dist-packages/stimfit is for
public ones, and stimfit is not even a module strictly speaking (lacking
__init__.py)

e.g. see for reference:
http://www.debian.org/doc/packaging-manuals/python-policy/ch-programs.html#s-current_version_progs

> Sorry for being unclear: stfio and stimfit are using the same file
> reading source code, but can't use the same binaries, mostly because
> some GUI elements such as progress dialogs get compiled for stimfit
> but not for stfio.

ah -- thanks for the explanation


> >   ... there would be ./usr/lib/stimfit/libstf.so  which would
> >   absorbs all the code (e.g. like recording.*) which will be used (linked
> >   dynamically) by both _stf.so and bin/stimfit
> >   and definitions present in /usr/lib/stimfit/libstf.so would be defined
> I can't follow you here: _stf.so is now a symbolic link to
> libstf.so, i.e. both Python (via _stf.so) as well as bin/stimfit are
> using the same libstf.so

yes, and that one does not define some symbols which are known to it.

Let me just try to describe once again what I meant, although the whole
situation is probably more aiming clarity than necessary for
practicality, since stimfit is not to be used as an independent module, I guess
all those symbols become available at runtime since they are defined within
/usr/bin/stimfit binary which loads up libstf.so/_sft.so later on; which is
what I guess Yury was once trying to deliver to my tired mind ;):


Symbol _ZN9Recording9SetFitEndEi is for Recording::SetFitEnd, defined in
./src/core/recording.cpp and declared in ./src/core/recording.h.

Compiled stimfit-recording.o's get included into bin/stimfit and
libstfio.{a,so} but not into libstf.{a,so}, although declarations from
recording.h manage to get included (through #include's chain which I didn't
investigate) into libstf.{a,so}, which leads to those undefined symbols.

Since I do not know how to trigger usage of those symbols from within
stimfit's python shell (or either they are used at all), I do not know if there
is any effect or they get found due to the fact that python core is running
within stimfit process having them defined.

> >If not used it could simply be Suggests or absent at all ;-)
> Fixed (r471)
> >besides being legal information on original dates of copyright, it often
> >gives an idea on how old project(s) are ;-)
> Added (r471)
> >some are better than nothing -- so what about test.h5 file?
> Added to repository (r472).
coolio...

ok -- since per se I do not see any show-stoppers any longer and
packaging would be lintian clean -- please provide with a url to the fresh .dsc
with all those changed incorporated and we will upload it to Debian NEW.

I have filed an ITP (since there were none yet) on your behalf, and will
leave you a pleasure to close it ;)

Corresponding changelog entry should have "unstable" as the release, obviously
no ubuntu suffixes (for backports in NeuroDebian repository they will be added
automatically, e.g. see below) and should Close that ITP with "(Closes:
#612375)".

Meanwhile I have uploaded following builds to neuro.debian.net repository, and
http://neuro.debian.net/pkgs/stimfit.html page should reflect their presence
upon next rebuild.  Following "backports" were built/uploaded:

stimfit_0.10.8-0ubuntu2~nd60+1_i386.build   OK
stimfit_0.10.8-0ubuntu2~nd60+1_amd64.build  OK
stimfit_0.10.8-0ubuntu2~nd+1_i386.build OK
stimfit_0.10.8-0ubuntu2~nd+1_amd64.build    OK
stimfit_0.10.8-0ubuntu2~nd10.10+1_i386.build    OK
stimfit_0.10.8-0ubuntu2~nd10.10+1_amd64.build   OK
stimfit_0.10.8-0ubuntu2~nd10.04+1_i386.build    OK
stimfit_0.10.8-0ubuntu2~nd10.04+1_amd64.build   OK
stimfit_0.10.8-0ubuntu2~nd09.04+1_i386.build    OK
stimfit_0.10.8-0ubuntu2~nd09.04+1_amd64.build   OK

nd60 -- Debian squeeze, just nd -- sid
nd10,09 -- ubuntu releases

thanks for good work! Stay in touch ;)

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Yaroslav Halchenko                 www.ohloh.net/accounts/yarikoptic